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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ), 'gf_id' => 'HOM05D001235', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001235' ), 'data_identifier' => 'HOM05D001235', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001235', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '504', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p39300' => 'bna', 'A03p33550' => 'bna', 'A05p43150' => 'bna', 'A05p43160' => 'bna', 'A09p05820' => 'bna', 'A09p05840' => 'bna', 'Aa31LG11G10120' => 'aar', 'Aa31LG11G10130' => 'aar', 'Aa31LG5G14730' => 'aar', 'Actinidia33667' => 'ach', 'Actinidia35919' => 'ach', 'Ah.04g149690' => 'amhyb', 'AL3G14250' => 'aly', 'AL6G38320' => 'aly', 'AL6G38340' => 'aly', 'Aqoxy4G01016' => 'aox', 'Aqoxy5G00036' => 'aox', 'Aqoxy5G00539' => 'aox', 'Aqoxy5G00614' => 'aox', 'Aqoxy7G00751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.GJ28M3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I05DEU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I3JYC0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I7RWJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JRB4HK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7XCE3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MZNG30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RP8YTM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UX6RQI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W69CPD' => 'arhy', 'AT3G04270' => 'ath', 'AT3G04280' => 'ath', 'AT5G26570' => 'ath', 'AT5G26594' => 'ath', 'ATR0215G018' => 'atr', 'ATR0686G153' => 'atr', 'ATR0743G090' => 'atr', 'Atru.chr2.1136' => 'acertr', 'Atru.chr2.1992' => 'acertr', 'Atru.chr3.1828' => 'acertr', 'Atru.chr5.1928' => 'acertr', 'AUR62011957' => 'cqu', 'AUR62011958' => 'cqu', 'AUR62015280' => 'cqu', 'AUR62018504' => 'cqu', 'AUR62020915' => 'cqu', 'AUR62024518' => 'cqu', 'AUR62024520' => 'cqu', 'AUR62026109' => 'cqu', 'AUR62026111' => 'cqu', 'AUR62026112' => 'cqu', 'AUR62032270' => 'cqu', 'AUR62032271' => 'cqu', 'AUR62032728' => 'cqu', 'AUR62043531' => 'cqu', 'AUR62044464' => 'cqu', 'AUR62044465' => 'cqu', 'BcaB04g19344' => 'bca', 'BcaB04g19732' => 'bca', 'BcaB04g19735' => 'bca', 'BcaB07g29956' => 'bca', 'BcaB07g29957' => 'bca', 'BcaC01g04383' => 'bca', 'BcaC03g16071' => 'bca', 'BcaC03g17860' => 'bca', 'BcaC03g17861' => 'bca', 'BcaC04g23551' => 'bca', 'BcaC04g23557' => 'bca', 'BcaC04g23619' => 'bca', 'BcaC05g29955' => 'bca', 'BcaC05g29956' => 'bca', 'BcaC05g30207' => 'bca', 'BcaC05g30208' => 'bca', 'BcaNung03966' => 'bca', 'BcaNung04232' => 'bca', 'BcaNung04233' => 'bca', 'BolC2t11957H' => 'bol', 'BolC3t16343H' => 'bol', 'BolC4t22855H' => 'bol', 'BolC5t34944H' => 'bol', 'BolC5t34945H' => 'bol', 'BolC6t37532H' => 'bol', 'BolC9t53562H' => 'bol', 'BolC9t53563H' => 'bol', 'BraA02t08895Z' => 'bra', 'BraA03t12530Z' => 'bra', 'BraA05t23057Z' => 'bra', 'BraA06t26602Z' => 'bra', 'BraA09t36223Z' => 'bra', 'BraA09t36226Z' => 'bra', 'C01p51380' => 'bna', 'C02p59020' => 'bna', 'C03p40750' => 'bna', 'C05p62890' => 'bna', 'C05p62900' => 'bna', 'C09p06430' => 'bna', 'CAN.G439.7' => 'can', 'CAN.G681.26' => 'can', 'CANSAT01G0638' => 'cansat', 'CANSAT01G1725' => 'cansat', 'CANSAT01G3094' => 'cansat', 'CANSAT54G0425' => 'cansat', 'CANSAT78G1591' => 'cansat', 'CARHR078420' => 'chi', 'CARHR078430' => 'chi', 'CARHR187030' => 'chi', 'CARHR187040' => 'chi', 'Carub.0002s1101' => 'cru', 'Carub.0003s0348' => 'cru', 'Carub.0003s0349' => 'cru', 'Carub.0006s2413' => 'cru', 'Carub.0006s2414' => 'cru', 'Ca_08754_v3' => 'car', 'Ca_08770_v3' => 'car', 'Ca_11427_v3' => 'car', 'Ca_29863_v3' => 'car', 'CBR_g30239' => 'cbr', 'Cc03_g10000' => 'ccan', 'CDE02G3575' => 'cde', 'CDE04G0849' => 'cde', 'CDE07G0946' => 'cde', 'CDE07G1609' => 'cde', 'Cfa002519' => 'cfa', 'Cfa002520' => 'cfa', 'Cfa002521' => 'cfa', 'Cfa006306' => 'cfa', 'Cfa008685' => 'cfa', 'Cfa017722' => 'cfa', 'Cfa017723' => 'cfa', 'Cfa017724' => 'cfa', 'Ciclev10004968m.g' => 'ccl', 'Ciclev10006658m.g' => 'ccl', 'Ciclev10006814m.g' => 'ccl', 'Ciclev10006872m.g' => 'ccl', 'Ciclev10017880m.g' => 'ccl', 'Ciclev10024122m.g' => 'ccl', 'CiPaw.01G110000' => 'cil', 'CiPaw.03G153300' => 'cil', 'CiPaw.04G108400' => 'cil', 'CiPaw.04G108500' => 'cil', 'CiPaw.14G082700' => 'cil', 'ClCG07G015490' => 'cla', 'ClCG11G010210' => 'cla', 'COL.COLO4_03859' => 'col', 'COL.COLO4_03862' => 'col', 'COL.COLO4_03864' => 'col', 'COL.COLO4_08688' => 'col', 'COL.COLO4_08689' => 'col', 'COL.COLO4_10349' => 'col', 'COL.COLO4_12040' => 'col', 'COL.COLO4_13957' => 'col', 'COL.COLO4_37866' => 'col', 'COL.COLO4_38181' => 'col', 'Cpa.g.sc502.2' => 'cpa', 'Cpa.g.sc51.33' => 'cpa', 'Cpa.g.sc8.202' => 'cpa', 'Cpa.g.sc8.203' => 'cpa', 'Cpa.g.sc8.311' => 'cpa', 'Cre17.g719900' => 'cre', 'CsaV3_4G003110' => 'csa', 'CSS0005175' => 'camsi', 'CSS0008762' => 'camsi', 'CSS0015752' => 'camsi', 'CSS0039330' => 'camsi', 'DCAR_000870' => 'dca', 'DCAR_000872' => 'dca', 'DCAR_000873' => 'dca', 'DCAR_000874' => 'dca', 'DCAR_000875' => 'dca', 'DCAR_005326' => 'dca', 'DCAR_005648' => 'dca', 'DCAR_005650' => 'dca', 'DCAR_005672' => 'dca', 'DCAR_005740' => 'dca', 'DCAR_010844' => 'dca', 'DCAR_016374' => 'dca', 'DCAR_016377' => 'dca', 'DCAR_020768' => 'dca', 'DCAR_027478' => 'dca', 'DCAR_029520' => 'dca', 'Dinv13678' => 'din', 'Dinv15892' => 'din', 'Dinv27164' => 'din', 'Dinv32201' => 'din', 'Duzib128G1418' => 'dzi', 'Duzib138G0593' => 'dzi', 'Duzib138G1895' => 'dzi', 'Duzib151G0601' => 'dzi', 'Duzib177G0932' => 'dzi', 'Duzib211G0589' => 'dzi', 'Duzib212G0549' => 'dzi', 'ECA248G1402' => 'eca', 'EL10Ac3g07148' => 'bvu', 'EL10Ac3g07409' => 'bvu', 'EL10Ac5g10480' => 'bvu', 'Eucgr.B02165' => 'egr', 'Eucgr.B02166' => 'egr', 'Eucgr.B02167' => 'egr', 'Eucgr.C02019' => 'egr', 'Eucgr.F03685' => 'egr', 'Eucgr.F03686' => 'egr', 'Eucgr.H00494' => 'egr', 'Eucgr.H00820' => 'egr', 'Eucgr.H00821' => 'egr', 'Eucgr.H00822' => 'egr', 'Eucgr.H04198' => 'egr', 'FAN05G0439' => 'fan', 'FAN05G4036' => 'fan', 'FAN05G4843' => 'fan', 'FAN07G2568' => 'fan', 'FAN09G0578' => 'fan', 'FAN09G3685' => 'fan', 'FAN12G0235' => 'fan', 'FAN14G0714' => 'fan', 'FAN14G5587' => 'fan', 'FAN15G3635' => 'fan', 'FAN15G3742' => 'fan', 'FAN17G0427' => 'fan', 'FAN22G1075' => 'fan', 'FAN24G1954' => 'fan', 'FAN24G2146' => 'fan', 'FAN27G2703' => 'fan', 'FvH4_2g19810' => 'fve', 'FvH4_2g19811' => 'fve', 'FvH4_2g19840' => 'fve', 'FvH4_4g12510' => 'fve', 'FvH4_6g01360' => 'fve', 'Glyma.03G170100' => 'gma', 'Glyma.03G170200' => 'gma', 'Glyma.10G298000' => 'gma', 'Glyma.19G169700' => 'gma', 'Glyma.19G171300' => 'gma', 'Glyma.19G171400' => 'gma', 'Glyma.19G250500' => 'gma', 'Glyma.20G249000' => 'gma', 'Gohir.A05G276232' => 'ghi', 'Gohir.A07G202150' => 'ghi', 'Gohir.A07G202200' => 'ghi', 'Gohir.A07G202250' => 'ghi', 'Gohir.A08G105701' => 'ghi', 'Gohir.A08G192900' => 'ghi', 'Gohir.A09G209000' => 'ghi', 'Gohir.A10G133100' => 'ghi', 'Gohir.D07G208350' => 'ghi', 'Gohir.D07G208400' => 'ghi', 'Gohir.D07G208450' => 'ghi', 'Gohir.D08G116200' => 'ghi', 'Gohir.D08G210900' => 'ghi', 'Gohir.D09G202400' => 'ghi', 'Gohir.D10G133800' => 'ghi', 'Gorai.001G235100' => 'gra', 'Gorai.001G235200' => 'gra', 'Gorai.001G235300' => 'gra', 'Gorai.004G125100' => 'gra', 'Gorai.004G223600' => 'gra', 'Gorai.006G226300' => 'gra', 'Gorai.009G291500' => 'gra', 'Gorai.011G147600' => 'gra', 'Gorai.013G189000' => 'gra', 'GSVIVG01014514001' => 'vvi', 'GSVIVG01026349001' => 'vvi', 'GSVIVG01028495001' => 'vvi', 'GSVIVG01031639001' => 'vvi', 'HanXRQChr01g0021711' => 'han', 'Haze_02578' => 'cav', 'Haze_04482' => 'cav', 'Haze_04491' => 'cav', 'Haze_11704' => 'cav', 'Haze_24743' => 'cav', 'Haze_24744' => 'cav', 'Hma1.2p1_0349F.1_g132360' => 'hma', 'Hma1.2p1_0689F.1_g203720' => 'hma', 'HPP92_009959' => 'vpl', 'HPP92_009960' => 'vpl', 'Hund19034' => 'sun', 'Lalb_Chr01g0019371' => 'lal', 'Lalb_Chr01g0019401' => 'lal', 'Lalb_Chr02g0144531' => 'lal', 'Lalb_Chr03g0035121' => 'lal', 'Lalb_Chr16g0388021' => 'lal', 'Lalb_Chr20g0113351' => 'lal', 'Lalb_Chr25g0289691' => 'lal', 'Lalb_Chr25g0289701' => 'lal', 'Lalb_Chr25g0289751' => 'lal', 'Lj1g0002527' => 'lja', 'Lj1g0016975' => 'lja', 'Lj1g0023506' => 'lja', 'Lj5g0010068' => 'lja', 'Lj6C311G3' => 'lonja', 'Lsat_1_v5_gn_1_69940' => 'lsa', 'Manes.05G194300' => 'mes', 'Manes.12G044300' => 'mes', 'Manes.13G042900' => 'mes', 'Mapoly0096s0069' => 'mpo', 'MBI07_g41650_MAGBIO' => 'mbi', 'MBI08_g09974_MAGBIO' => 'mbi', 'MBI08_g20600_MAGBIO' => 'mbi', 'MBI11_g00133_MAGBIO' => 'mbi', 'MCO03G064' => 'mco', 'MCO05G382' => 'mco', 'MCO13G077' => 'mco', 'MCO16G355' => 'mco', 'MD04G1025900' => 'mdo', 'MD05G1182700' => 'mdo', 'MD10G1170800' => 'mdo', 'Medtr0022s0450' => 'mtr', 'Medtr1g117000' => 'mtr', 'Medtr4g071650' => 'mtr', 'Medtr6g008860' => 'mtr', 'Medtr6g093240' => 'mtr', 'Medtr7g089310' => 'mtr', 'Medtr7g098860' => 'mtr', 'Medtr7g098910' => 'mtr', 'Medtr7g099500' => 'mtr', 'Medtr8g063580' => 'mtr', 'MELO3C017735.2' => 'cme', 'Migut.M01873' => 'egut', 'Migut.N03329' => 'egut', 'MSTRG.22434' => 'ama', 'Nitab4.5_0001219g0060' => 'nta', 'Nitab4.5_0001693g0060' => 'nta', 'Nitab4.5_0005439g0010' => 'nta', 'Nitab4.5_0007338g0010' => 'nta', 'Nitab4.5_0012294g0010' => 'nta', 'Nn1g08260' => 'nnu', 'Oeu001997.1' => 'oeu', 'Oeu058471.1' => 'oeu', 'Oeu060298.1' => 'oeu', 'Os03g0742300' => 'osa', 'Os04g0212450' => 'osa', 'Os12g0297500' => 'osa', 'Peaxi162Scf00217g00032' => 'pax', 'Peaxi162Scf00286g00547' => 'pax', 'PGR004G0353' => 'pgr', 'PGR083G1081' => 'pgr', 'PGR102G3214' => 'pgr', 'PGR142G1880' => 'pgr', 'PGR142G2388' => 'pgr', 'PGR142G4378' => 'pgr', 'PGSC0003DMG400013173' => 'stu', 'PGSC0003DMG400016613' => 'stu', 'PGSC0003DMG400035602' => 'stu', 'PGSC0003DMG400037096' => 'stu', 'PGSC0003DMG400039122' => 'stu', 'PGSC0003DMG400042470' => 'stu', 'PGSC0003DMG400044331' => 'stu', 'PGSC0003DMG400046048' => 'stu', 'PGSC0003DMG400046374' => 'stu', 'Phvul.001G166700' => 'pvu', 'Phvul.001G166800' => 'pvu', 'Phvul.001G168500' => 'pvu', 'Phvul.006G107500' => 'pvu', 'Phvul.007G001400' => 'pvu', 'Potri.001G050800' => 'ptr', 'Potri.001G050900' => 'ptr', 'Potri.001G051000' => 'ptr', 'Potri.001G055500' => 'ptr', 'Potri.001G055600' => 'ptr', 'Potri.002G234500' => 'ptr', 'Potri.002G253000' => 'ptr', 'Potri.002G253100' => 'ptr', 'Potri.003G172200' => 'ptr', 'Potri.003G172750' => 'ptr', 'Potri.003G172866' => 'ptr', 'Potri.003G172932' => 'ptr', 'Potri.003G177300' => 'ptr', 'Potri.003G177400' => 'ptr', 'Potri.009G108000' => 'ptr', 'Potri.014G147900' => 'ptr', 'Potri.019G024900' => 'ptr', 'Potri.019G025000' => 'ptr', 'Pp3c14_19150' => 'ppa', 'Pp3c17_18900' => 'ppa', 'Pp3c18_14870' => 'ppa', 'Pp3c22_16753' => 'ppa', 'PRCOL_00000902' => 'pco', 'Prupe.1G175200' => 'ppe', 'Prupe.8G209300' => 'ppe', 'Psat0s1999g0080' => 'psa', 'Psat1g078800' => 'psa', 'Psat3g039720' => 'psa', 'Psat3g050080' => 'psa', 'Psat3g051200' => 'psa', 'Psat3g051240' => 'psa', 'Psat3g051360' => 'psa', 'Psat3g052800' => 'psa', 'Psat6g244000' => 'psa', 'Psat7g099480' => 'psa', 'Psat7g227680' => 'psa', 'PSO170G5672' => 'pso', 'PSO357G0146' => 'pso', 'PSO384G2251' => 'pso', 'PSO407G0374' => 'pso', 'PSO675G4108' => 'pso', 'PSO675G5202' => 'pso', 'PSO732G0343' => 'pso', 'PSO732G0465' => 'pso', 'QL06p027955' => 'qlo', 'QL08p008692' => 'qlo', 'QL09p043992' => 'qlo', 'QL09p044005' => 'qlo', 'QL09p044015' => 'qlo', 'QL09p044033' => 'qlo', 'QL09p044061' => 'qlo', 'QL09p044250' => 'qlo', 'QL12p022339' => 'qlo', 'RcHm_v2.0_Chr3g0448931' => 'rch', 'RcHm_v2.0_Chr4g0411211' => 'rch', 'RcHm_v2.0_Chr4g0411251' => 'rch', 'RcHm_v2.0_Chr4g0411331' => 'rch', 'RcHm_v2.0_Chr6g0285521' => 'rch', 'RcHm_v2.0_Chr6g0285531' => 'rch', 'RcHm_v2.0_Chr6g0285541' => 'rch', 'Rhsim01G0114000' => 'rsi', 'Rhsim13G0119300' => 'rsi', 'Sabra01G0035500' => 'sbr', 'Sabra01G0035600' => 'sbr', 'Sabra01G0040100' => 'sbr', 'Sabra02G0178900' => 'sbr', 'Sabra02G0192200' => 'sbr', 'Sabra02G0192300' => 'sbr', 'Sabra03G0126000' => 'sbr', 'Sabra03G0126400' => 'sbr', 'Sabra03G0129900' => 'sbr', 'Sabra03G0130000' => 'sbr', 'Sabra09G0082400' => 'sbr', 'Sabra14G0111700' => 'sbr', 'Sabra15G0057800' => 'sbr', 'Sabra19G0034600' => 'sbr', 'SalBow2G0322' => 'sbo', 'SalBow6G1240' => 'sbo', 'Sc17g0001040' => 'sci', 'Sc17g0001050' => 'sci', 'Sc17g0001070' => 'sci', 'Sc17g0001080' => 'sci', 'Sc17g0001090' => 'sci', 'Sc17g0001100' => 'sci', 'Sc17g0001120' => 'sci', 'Sc17g0002470' => 'sci', 'Sc17g0002960' => 'sci', 'Sc19g0007540' => 'sci', 'Sc19g0007550' => 'sci', 'Sed0003584' => 'sed', 'Sed0023516' => 'sed', 'SEGI_29879' => 'sgi', 'SGA_v2.0_scaffold223G42840' => 'sas', 'SGA_v2.0_scaffold28G12047' => 'sas', 'SHI14806' => 'shi', 'SHI14818' => 'shi', 'SMO146G0043' => 'smo', 'SMO239G0026' => 'smo', 'Solyc03g071535.1' => 'sly', 'Solyc09g098040.3' => 'sly', 'Solyc11g071630.1' => 'sly', 'Sopen09g035960' => 'spe', 'Sopen11g029300' => 'spe', 'Sp2g21440' => 'spa', 'Sp2g21450' => 'spa', 'Sp3g03180' => 'spa', 'TAR362G0194' => 'tar', 'TAR362G0786' => 'tar', 'TAR362G1105' => 'tar', 'TAR365G0591' => 'tar', 'TAR365G1112' => 'tar', 'TAR636G0101' => 'tar', 'THA.LOC104818773' => 'tha', 'THA.LOC104819130' => 'tha', 'THA.LOC104820076' => 'tha', 'THA.LOC104820755' => 'tha', 'THA.LOC104822294' => 'tha', 'Thecc.01G236400' => 'tca', 'Thecc.01G236500' => 'tca', 'Thecc.02G225000' => 'tca', 'Thecc.04G188100' => 'tca', 'Thecc.05G265000' => 'tca', 'Thhalv10003634m.g' => 'esa', 'Thhalv10005298m.g' => 'esa', 'Thhalv10022233m.g' => 'esa', 'TPR.G11477' => 'tpr', 'TPR.G18917' => 'tpr', 'TPR.G20056' => 'tpr', 'TPR.G32566' => 'tpr', 'TPR.G32597' => 'tpr', 'TPR.G40064' => 'tpr', 'TPR.G40801' => 'tpr', 'TPR.G671' => 'tpr', 'TPR.G7564' => 'tpr', 'TPR.G8889' => 'tpr', 'TPR.G9144' => 'tpr', 'TWI14G1144' => 'twi', 'TWI34G0360' => 'twi', 'TWI59G0690' => 'twi', 'TWI73G0237' => 'twi', 'unitig_21.g20191' => 'ugi', 'vmacro03416' => 'vma', 'vmacro20797' => 'vma', 'VMungo0540G0715' => 'vmu', 'VMungo0720G0937' => 'vmu', 'VMungo1184G0001' => 'vmu', 'VMungo1383G0973' => 'vmu', 'VMungo1383G2462' => 'vmu', 'Zm00001eb056810' => 'zma', 'Zm00001eb088320' => 'zma', 'Zm00001eb409850' => 'zma' ) $gf_id = 'HOM05D001235' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001235' ) $data_identifier = 'HOM05D001235' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 16, 'bca' => (int) 19, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 2, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 4, 'cfa' => (int) 8, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 10, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 4, 'dca' => (int) 16, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 15, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 3, 'mtr' => (int) 10, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 3, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 6, 'stu' => (int) 9, 'pvu' => (int) 5, 'ptr' => (int) 18, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 11, 'pso' => (int) 8, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 2, 'sbr' => (int) 14, 'sbo' => (int) 2, 'sci' => (int) 11, 'sed' => (int) 2, 'sgi' => (int) 1, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 11, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb409850' $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